First of all, congrats on knowing who you are- you do not as it stands have to "convert" to atheism, you are an atheist. That's all. There is no sign-up sheet- you simply don't believe in god(s). Now, based on that, you have to make a choice, because it sounds like you stand to lose some connections if you choose to be open about who you are, and what you believe. I think, if you really care about this girl and if she cares about you, the most important thing here is honesty. Simply tell her you love her, but you can't change who you are. Obviously you accept her and her beliefs, so it's not like you're discriminating- you're just asking her not to discriminate against you. Pretending to be something you're clearly not is disingenuous, and if your relationship hinges on this point, only prolonging the inevitable.
To summarize that rambling: be open, and be truthful. My two cents.
To summarize that rambling: be open, and be truthful. My two cents.